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


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.


Coregonus maraena ACTB EEF1A1 GAPDH Housekeeping gene RPL9 RPL32 RPS20 Salmonidae 



Beta actin


Basic local alignment search tool


Elongation factor 1 alpha


Glyceraldehydes-3-phosphate dehydrogenase


Homo sapiens


Oncorhynchus mykiss


Ribosomal protein 9


Ribosomal protein 32


Ribosomal protein S20


Quantitative real-time PCR


Salmo salar



We thank Ingrid Hennings, Brigitte Schöpel and Luisa Falkenthal for their excellent technical assistance. This project of the Campus bioFISCH M-V is kindly funded and supported by the European Fisheries Fund (EFF) and the Ministry of Agriculture, the Environment and Consumer Protection Mecklenburg-Western Pomerania, Germany (Pilot project VI-560/730-32614). Campus bioFISCH M-V is a cooperation between the Leibniz Institute of Farm Animal Biology (Dummerstorf, Germany), Federal Research Institute for Animal Health (Riems, Germany), State Research Institute for Agriculture and Fishing in Born/Darß and several fish farms in Mecklenburg-Western Pomerania, Germany. The authors declare no conflict of interest.


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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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