Selection and validation of reference genes for real-time RT-PCR studies in the non-model species Delomys sublineatus, an endemic Brazilian rodent.
Quantitative real-time RT-PCR (qRT-PCR) is a sensitive technique for gene expression analysis. A critical factor for creating reliable data in relative quantification is the normalization of the expression data of genes of interest. Therefore the needed normalization factor is calculated out of the expression data of co-amplified genes that are stable expressed in the certain sample material, the so-called reference genes. In this study, we demonstrate the important process of validating potential reference genes using a non-model species. As there are almost no sequences known of the Pallid Atlantic Forest Rat (Delomys sublineatus), a rodent used as indicator species in conservation studies of the endangered Brazilian rainforest, suitable primer sets are more problematic to find than in model species. Out of nine tested primer sets designed for the fully sequenced Mus musculus, five could be used for the establishment of a proper running SYBR-Green assay and validation of their constant expression. qRT-PCR results of 12 cDNAs of Delomys livers were analyzed with three different validation software programs: BestKeeper, NormFinder and geNorm. Our approach showed that out of the five (Sdha, Canx, Pgk1, Actb and Actg1) potential reference genes, the first four should be used for accurate normalization in further relative quantification analyses. Transferring data from close-by model organisms makes high sensitive real-time RT-PCR applicable even to free-ranging non-model organisms. Our approach might be suitable for other non-model organisms.
Weyrich
Alexandra
A
Leibniz Institute for Zoo and Wildlife Research (IZW), Evolutionary Genetics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany.
Axtner
Jan
J
Sommer
Simone
S
D000818:Animals; D052160:Benzothiazoles; D001938:Brazil; D003247:Conservation of Natural Resources; D018076:DNA, Complementary / Q000235:genetics; D003959:Diamines; D056727:Endangered Species; D020869:Gene Expression Profiling; D005796:Genes; D051379:Mice; D009930:Organic Chemicals / Q000737:chemistry; D011804:Quinolines; D012333:RNA, Messenger / Q000235:genetics; D012015:Reference Standards; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000592:standards*; D016205:Sigmodontinae / Q000235:genetics*; D014197:Trees
D052160:Benzothiazoles; D018076:DNA, Complementary; D003959:Diamines; D009930:Organic Chemicals; D011804:Quinolines; D012333:RNA, Messenger; C098022:SYBR Green I