Display options
Cite
Marancik D, Gao G, Paneru B, et al. Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum. Front Genet. 2015;5:453doi: 10.3389/fgene.2014.00453.
Marancik, D., Gao, G., Paneru, B., Ma, H., Hernandez, A. G., Salem, M., Yao, J., Palti, Y., & Wiens, G. D. (2014). Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum. Frontiers in genetics, 5453. https://doi.org/10.3389/fgene.2014.00453
Marancik, David, et al. "Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum." Frontiers in genetics vol. 5 (2014): 453. doi: https://doi.org/10.3389/fgene.2014.00453
Marancik D, Gao G, Paneru B, Ma H, Hernandez AG, Salem M, Yao J, Palti Y, Wiens GD. Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum. Front Genet. 2015 Jan 08;5:453. doi: 10.3389/fgene.2014.00453. eCollection 2014. PMID: 25620978; PMCID: PMC4288049.
Copy Download .nbib Format: NLM
Share it on

Front Genet. 2015 Jan 08;5:453. doi: 10.3389/fgene.2014.00453. eCollection 2014.

Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum.

Frontiers in genetics

David Marancik, Guangtu Gao, Bam Paneru, Hao Ma, Alvaro G Hernandez, Mohamed Salem, Jianbo Yao, Yniv Palti, Gregory D Wiens

Affiliations

  1. National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture Kearneysville, WV, USA.
  2. Department of Biology, Middle Tennessee State University Murfreesboro, TN, USA.
  3. Animal and Nutritional Sciences, West Virginia University Morgantown, WV, USA.
  4. High-Throughput Sequencing and Genotyping Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign Urbana, IL, USA.

PMID: 25620978 PMCID: PMC4288049 DOI: 10.3389/fgene.2014.00453

Abstract

Genetic improvement for enhanced disease resistance in fish is an increasingly utilized approach to mitigate endemic infectious disease in aquaculture. In domesticated salmonid populations, large phenotypic variation in disease resistance has been identified but the genetic basis for altered responsiveness remains unclear. We previously reported three generations of selection and phenotypic validation of a bacterial cold water disease (BCWD) resistant line of rainbow trout, designated ARS-Fp-R. This line has higher survival after infection by either standardized laboratory challenge or natural challenge as compared to two reference lines, designated ARS-Fp-C (control) and ARS-Fp-S (susceptible). In this study, we utilized 1.1 g fry from the three genetic lines and performed RNA-seq to measure transcript abundance from the whole body of naive and Flavobacterium psychrophilum infected fish at day 1 (early time-point) and at day 5 post-challenge (onset of mortality). Sequences from 24 libraries were mapped onto the rainbow trout genome reference transcriptome of 46,585 predicted protein coding mRNAs that included 2633 putative immune-relevant gene transcripts. A total of 1884 genes (4.0% genome) exhibited differential transcript abundance between infected and mock-challenged fish (FDR < 0.05) that included chemokines, complement components, tnf receptor superfamily members, interleukins, nod-like receptor family members, and genes involved in metabolism and wound healing. The largest number of differentially expressed genes occurred on day 5 post-infection between naive and challenged ARS-Fp-S line fish correlating with high bacterial load. After excluding the effect of infection, we identified 21 differentially expressed genes between the three genetic lines. In summary, these data indicate global transcriptome differences between genetic lines of naive animals as well as differentially regulated transcriptional responses to infection.

Keywords: Flavobacterium psychrophilum; aquaculture; bacterial cold water disease; disease resistance; immune gene; rainbow trout genome; selective breeding; tnfrsf

References

  1. Res Vet Sci. 2000 Oct;69(2):165-9 - PubMed
  2. Dev Comp Immunol. 2001 Apr;25(3):205-17 - PubMed
  3. Fish Shellfish Immunol. 2001 Nov;11(8):673-82 - PubMed
  4. J Fish Dis. 2003 Oct;26(10):563-74 - PubMed
  5. Mar Biotechnol (NY). 2004 May-Jun;6(3):199-214 - PubMed
  6. Vet Immunol Immunopathol. 2004 Oct;101(3-4):211-22 - PubMed
  7. Nucleic Acids Res. 2005 Jan 12;33(1):272-9 - PubMed
  8. Int J Dev Neurosci. 2005 Feb;23(1):9-14 - PubMed
  9. Mol Immunol. 2006 Apr;43(11):1900-11 - PubMed
  10. Genome Inform. 2005;16(1):106-15 - PubMed
  11. J Fish Dis. 2006 Apr;29(4):215-24 - PubMed
  12. Fish Shellfish Immunol. 2007 Dec;23(6):1127-51 - PubMed
  13. Free Radic Biol Med. 2008 Feb 15;44(4):682-91 - PubMed
  14. J Immunol. 2008 Mar 15;180(6):4156-65 - PubMed
  15. Dev Comp Immunol. 2008;32(10):1160-9 - PubMed
  16. Nucleic Acids Res. 2008 Jun;36(10):3420-35 - PubMed
  17. Nat Methods. 2008 Jul;5(7):621-8 - PubMed
  18. Nat Protoc. 2008;3(6):1101-8 - PubMed
  19. J Anim Sci. 2009 Mar;87(3):860-7 - PubMed
  20. Genome Biol. 2009;10(3):R25 - PubMed
  21. Vet Immunol Immunopathol. 2009 Jul 15;130(1-2):120-4 - PubMed
  22. Dev Comp Immunol. 2010 May;34(5):491-500 - PubMed
  23. J Anim Sci. 2010 Jun;88(6):1936-46 - PubMed
  24. J Fish Dis. 2011 May;34(5):403-8 - PubMed
  25. Dev Comp Immunol. 2011 Dec;35(12):1263-72 - PubMed
  26. Dev Comp Immunol. 2011 Dec;35(12):1324-35 - PubMed
  27. Fish Shellfish Immunol. 2011 Sep;31(3):491-9 - PubMed
  28. Vet Immunol Immunopathol. 2012 Mar 15;146(1):8-17 - PubMed
  29. PLoS One. 2012;7(6):e39126 - PubMed
  30. Fish Shellfish Immunol. 2012 Oct;33(4):1008-15 - PubMed
  31. Vet Microbiol. 2013 Feb 22;162(1):127-35 - PubMed
  32. FEMS Microbiol Lett. 2013 Feb;339(2):122-9 - PubMed
  33. Mol Immunol. 2013 Dec;56(4):317-27 - PubMed
  34. PLoS One. 2013 Oct 09;8(10):e75749 - PubMed
  35. Mar Biotechnol (NY). 2014 Jun;16(3):349-60 - PubMed
  36. Nat Commun. 2014 Apr 22;5:3657 - PubMed
  37. Mol Immunol. 2014 Sep;61(1):44-53 - PubMed
  38. Microb Biotechnol. 2014 Sep;7(5):414-23 - PubMed
  39. PLoS One. 2014 Aug 06;9(8):e104509 - PubMed
  40. J Aquat Anim Health. 2014 Sep;26(3):181-9 - PubMed
  41. Genome Announc. 2014 Sep 18;2(5):null - PubMed
  42. Dis Aquat Organ. 2014 Oct 16;111(3):239-48 - PubMed
  43. Genome Biol. 2014;15(12):550 - PubMed
  44. J Fish Dis. 2015 Mar;38(3):259-70 - PubMed
  45. FASEB J. 1994 Oct;8(13):1041-7 - PubMed
  46. Nat Med. 1996 Mar;2(3):287-92 - PubMed
  47. Trends Cell Biol. 1998 May;8(5):189-92 - PubMed
  48. Immunol Rev. 1998 Dec;166:39-57 - PubMed

Publication Types