title: Determination of reference microRNAs for relative quantification in grass carp (Ctenopharyngodon idella).
abstract: Relative quantification is the strategy of choice for processing real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) data in microRNA (miRNA) expression studies. Normalization of relative quantification data is performed by comparison to reference genes. In teleost species, such as grass carp (Ctenopharyngodon idella), the determination of reference miRNAs and the optimal numbers of these that should be used has not been widely studied. In the present study, the stability of seven miRNAs (miR-126-3p, miR-101a, miR-451, miR-22a, miR-146, miR-142a-5p and miR-192) was investigated by RT-qPCR in different tissues and in different development stages of grass carp. Stability values were calculated with geNorm, NormFinder, BestKeeper and Delta CT algorithms. The results showed that tissue type is an important variability factor for miRNA expression stability. All seven miRNAs had good stability values and, therefore, could be used as reference miRNAs. When all tissues and developmental stages were considered, miR-101a was the most stable miRNA. When each tissue type was considered separately, the most stable miRNAs were 126-3p in blood and liver, 101a in the gills, 192 in the kidney, 451 in the intestine and 22a in the brain, head kidney, spleen, heart, muscle, skin and fin. 126-3p was the most stable reference miRNA gene during developmental stages 1-5, while 22a was the most stable during developmental stages 6-18. Overall, this study provides valuable information about the reference miRNAs that can be used to perform appropriate normalizations when undertaking relative quantification in RT-qPCR studies of grass carp.
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China.
authors.forename: Xiao-Yan
authors.initials: XY
authors.lastname: Xu
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China.
authors.forename: Yu-Bang
authors.initials: YB
authors.lastname: Shen
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China.
authors.forename: Jian-Jun
authors.initials: JJ
authors.lastname: Fu
authors.affiliation: National Pathogen Collection Center for Aquatic Animals, College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, 201306 Shanghai, PR China.
authors.forename: Li-Qun
authors.initials: LQ
authors.lastname: Lu
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China; E-Institute of Shanghai Universities, Shanghai Ocean University, 999 Huchenghuan Road, 201306 Shanghai, PR China. Electronic address: jlli2009@126.com.
authors.forename: Jia-Le
authors.initials: JL
authors.lastname: Li
mesh_terms: D000818:Animals; D002347:Carps / Q000196:embryology / Q000235:genetics* / Q000254:growth & development / Q000276:immunology; D004625:Embryo, Nonmammalian / Q000378:metabolism; D015870:Gene Expression; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism*; D009928:Organ Specificity; D060888:Real-Time Polymerase Chain Reaction / Q000662:veterinary; D012016:Reference Values; D017422:Sequence Analysis, DNA / Q000662:veterinary
chemical_list: D035683:MicroRNAs
keywords: Grass carp; Internal control; MicroRNA; Real-time PCR