Fish Physiology and Biochemistry

, Volume 41, Issue 2, pp 397–412 | Cite as

Identification and de novo sequencing of housekeeping genes appropriate for gene expression analyses in farmed maraena whitefish (Coregonus maraena) during crowding stress

  • Simone Altmann
  • Alexander Rebl
  • Carsten Kühn
  • Tom Goldammer
Article

Abstract

Maraena whitefish (Coregonus maraena; synonym Coregonus lavaretus f. balticus) is a high-quality food fish in the Southern Baltic Sea belonging to the group of salmonid fishes. Coregonus sp. is successfully kept in aquaculture throughout northern Europe (e.g. in Finland, Germany, Russia) and North America. In this regard, the molecular and immunological characterisation of stress response in maraena whitefish contributes to the development of robust and fast-growing maraena whitefish breeding strains for aquaculture. Thus, in the present study, the potential housekeeping genes beta actin (ACTB), elongation factor 1 alpha (EEF1A1), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), ribosomal protein 9 (RPL9), ribosomal protein 32 (RPL32) and ribosomal protein S20 (RPS20) were de novo sequenced and tested concerning their applicability as reference genes in quantitative real-time PCR (qPCR) in maraena whitefish under different stocking densities. For this purpose, tissue samples of liver, kidney, gills, head kidney, skin, adipose tissue, heart and dorsal fin were investigated. qPCR data were analysed with Normfinder tool to determine gene expression stability. DNA sequencing exposed transcribed paralogous EEF1A1A and EEF1A1B genes differing in their putative protein structure. Normfinder analysis revealed RPL9 and RPL32 as most stable, GAPDH and ACTB as least stable genes for qPCR analyses, respectively. This is the first study that provides a subset of seven de novo sequenced housekeeping genes usable as reference genes in studies of stress response in maraena whitefish.

Keywords

Coregonus maraena ACTB EEF1A1 GAPDH Housekeeping gene RPL9 RPL32 RPS20 Salmonidae 

Abbreviations

ACTB

Beta actin

BLAST

Basic local alignment search tool

EEF1A1

Elongation factor 1 alpha

GAPDH

Glyceraldehydes-3-phosphate dehydrogenase

HSA

Homo sapiens

OMY

Oncorhynchus mykiss

RPL9

Ribosomal protein 9

RPL32

Ribosomal protein 32

RPS20

Ribosomal protein S20

qPCR

Quantitative real-time PCR

SSA

Salmo salar

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Simone Altmann
    • 1
  • Alexander Rebl
    • 1
  • Carsten Kühn
    • 2
  • Tom Goldammer
    • 1
  1. 1.Fish Genetics Unit, Institute for Genome BiologyLeibniz Institute for Farm Animal Biology (FBN)DummerstorfGermany
  2. 2.Institute for FisheryState Research Institute for Agriculture and Fishing (LFA M-V)BornGermany

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