Validation of housekeeping genes as candidate internal references for quantitative expression studies in healthy and nervous necrosis virus-infected seven-band grouper (Hyporthodus septemfasciatus)

• Published in: Fisheries and aquatic sciences Vol. 22; no. 1; pp. 1 - 8
• Main Authors: Krishnan, Rahul, Qadiri, Syed Shariq Nazir, Kim, Jong-Oh, Kim, Jae-Ok, Oh, Myung-Joo
• Format: Journal Article
• Language: English
• Published: Springer 10-12-2019; The Korean Society of Fisheries and Aquatic Science
• Subjects: Actin; Algorithms; Analysis; Biological response modifiers; Expression stability; Fishes; Genes; Genetic research; Health aspects; Housekeeping gene; Interferon; Medical research; Monosaccharides; Muscle proteins; Necrosis; Nervous necrosis virus; Phosphates; Rankings; RT-qPCR
• ISSN: 2234-1757; 2234-1749; 2234-1757
• DOI: 10.1186/s41240-019-0142-3

Background In the present study, we evaluated four commonly used housekeeping genes, viz., actin-[beta], elongation factor-1[alpha] (EF1[alpha]), acidic ribosomal protein (ARP), and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as internal references for quantitative analysis of immune genes in nervous necrosis virus (NNV)-infected seven-band grouper, Hyporthodus septemfasciatus. Methods Expression profiles of the four genes were estimated in 12 tissues of healthy and infected seven-band grouper. Expression stability of the genes was calculated using the delta Ct method, BestKeeper, NormFinder, and geNorm algorithms. Consensus ranking was performed using RefFinder, and statistical analysis was done using GraphpadPrism 5.0. Results Tissue-specific variations were observed in the four tested housekeeping genes of healthy and NNV-infected seven-band grouper. Fold change calculation for interferon-1 and Mx expression using the four housekeeping genes as internal references presented varied profiles for each tissue. EF1[alpha] and actin-[beta] was the most stable expressed gene in tissues of healthy and NNV-infected seven-band grouper, respectively. Consensus ranking using RefFinder suggested EF1[alpha] as the least variable and highly stable gene in the healthy and infected animals. Conclusions These results suggest that EF1[alpha] can be a fairly better internal reference in comparison to other tested genes in this study during the NNV infection process. This forms the pilot study on the validation of reference genes in Hyporthodus septemfasciatus, in the context of NNV infection. Keywords: Housekeeping gene, Expression stability, RT-qPCR, Nervous necrosis virus