Evaluation of candidate reference genes in Q-PCR studies of Atlantic cod (Gadus morhua) ontogeny, with emphasis on the gastrointestinal tract

Abstract

To obtain reliable relative qPCR data in developing fish larvae, stable reference genes have to be found. This study is focused on finding good candidates for normalization of qPCR data for ontogenetic studies of Atlantic cod. Ten commonly used reference genes; Acidic ribosomal protein, Actin-related protein 2, beta-actin, Elongation factor 1 A, Glyceraldehyde-3-phosphate dehydrogenase, Ribosomal protein 37, Ribosomal protein 4, Ribosomal protein S9, beta 2-Tubulin and Ubiquitin were analyzed in developing larvae from 3 to 97 day post hatch (DPH). Two different tools were used to evaluate the stabilities of these genes; the geNorm software ranks the most stable genes based on a pair-wise analysis whereas NormFinder uses a model-based approach. The same genes were also analyzed in GI tract homogenates and compared to whole larvae homogenates. During Atlantic cod larval development there are several strong candidates with Ubiquitin as the most stable. The ribosomal proteins RPL4 and RPS9 are also strong candidates. RPL37 may be used but only when normalizing qRT-PCR results from one type of tissue. We also suggest the use of multiple genes for normalization of qRT-PCR. Our study suggests that whole-larvae samples can be used to study relative expression of genes that are expressed only in certain tissues.