scholarly journals Evaluation of potential reference genes for quantitative RT-PCR analysis in spotted sea bass (Lateolabrax maculatus) under normal and salinity stress conditions

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5631 ◽  
Author(s):  
Haolong Wang ◽  
Haishen Wen ◽  
Yun Li ◽  
Kaiqiang Zhang ◽  
Yang Liu
Keyword(s):  
Salinity Stress ◽  
Reference Genes ◽  
18S Rrna ◽  
Sea Bass ◽  
Stress Conditions ◽  
Pcr Analysis ◽  
Stable Gene ◽  
Qrt Pcr ◽  
Lateolabrax Maculatus ◽  
Suitable Reference

The aim of this study was to select the most suitable reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) of spotted sea bass (Lateolabrax maculatus), an important commercial marine fish in Pacific Asia, under normal physiological and salinity stress conditions. A total of 9 candidate reference genes (HPRT, GAPDH, EF1A, TUBA, RPL7, RNAPol II, B2M, ACTB and 18S rRNA) were analyzed by qRT-PCR in 10 tissues (intestine, muscle, stomach, brain, heart, liver, gill, kidney, pectoral fins and spleen) of L. maculatus. Four algorithms, geNorm, NormFinder, BestKeeper, and comparative ΔCt method, were used to evaluate the expression stability of the candidate reference genes. The results showed the 18S rRNA was most stable in different tissues under normal conditions. During salinity stress, RPL7 was the most stable gene according to overall ranking and the best combination of reference genes was RPL7 and RNAPol II. In contrast, GAPDH was the least stable gene which was not suitable as reference genes. The study showed that different algorithms might generate inconsistent results. Therefore, the combination of several reference genes should be selected to accurately calibrate system errors. The present study was the first to select reference genes of L. maculatus by qRT-PCR and provides a useful basis for selecting the appropriate reference gene in L. maculatus. The present study also has important implications for gene expression and functional genomics research in this species or other teleost species.

scholarly journals Identification And Evaluation of Reference Genes For Cynanchum Auriculatum Under Various Stress Conditions

2022 ◽  
Author(s):  
Zhi-Peng Zhu ◽  
Jian-Xiang Yu ◽  
Ke-Xin Wu ◽  
Qin-Yi Xu ◽  
Yi-Jun Kang ◽  
...  
Keyword(s):  
Reference Genes ◽  
Herbal Medicines ◽  
Stress Conditions ◽  
Pcr Analysis ◽  
Expression Stability ◽  
Qrt Pcr ◽  
Chinese Herbal ◽  
Cynanchum Auriculatum ◽  
Screening Study ◽  
Suitable Reference

Abstract Baishouwu (Cynanchum auriculatum) is a kind of critical Chinese herbal medicine. However, compared with the studies of other Chinese herbal medicines, the screening study on the reference genes of C. auriculatum is still the blank. Deterioration of the natural environment severely affects the growth and development of C. auriculatum. This study screened and identified suitable reference genes of C. auriculatum under various stress conditions. Based on qRT-PCR, geNorm, NormFinder, BestKeeper, and RefFinder were used for the expression stability evaluation of 12 potential reference genes from C. auriculatum. The ranking table showed that optimal reference genes included EF2 and SAMDC (heat stress), CYP and TUB-β (cold stress), TUB-α and GAPDH (drought stress), SAMDC and TUB-α (waterlogging stress), along with EF2 and ACT7 (salt stress). These results also demonstrated that under different abiotic stresses, suitable reference genes of plants should be selected for qRT-PCR analysis.

Selection of suitable reference genes for qRT-PCR analysis of Begonia semperflorens under stress conditions

2019 ◽  
Vol 46 (6) ◽  
pp. 6027-6037 ◽  
Author(s):  
Yanman Li ◽  
Ying Qu ◽  
Yang Wang ◽  
Xue Bai ◽  
Geng Tian ◽  
...  
Keyword(s):  
Reference Genes ◽  
Stress Conditions ◽  
Pcr Analysis ◽  
Qrt Pcr ◽  
Suitable Reference ◽  
Selection Of ◽  
Begonia Semperflorens

Selection and validation of reference genes for RT-qPCR analysis in Litchi chinensis Sonn. pericarp

2020 ◽  
Author(s):  
Fang Li ◽  
Jinhua Sun ◽  
Jiali Men ◽  
Huanling Li ◽  
Guo Wang ◽  
...  
Keyword(s):  
Reference Gene ◽  
Reference Genes ◽  
Negative Impact ◽  
Pcr Analysis ◽  
Stable Gene ◽  
Litchi Chinensis ◽  
Qrt Pcr ◽  
Pericarp Browning ◽  
Suitable Reference ◽  
Litchi Pericarp

Abstract Background: Quantitative real time PCR (qRT-PCR) is an important tool for gene expression analysis and function identification. Suitable reference genes are the basis of accurate and reliable qPCR results. Litchi ( Litchi chinensis Sonn.) is a commercially important tropical and subtropical fruit crop, rapid pericarp browning is the major negative impact on the industry. Reference gene validation would help screen for genes involved in the browning mechanism.Results: In this study, fifteen new candidate reference genes, identified with transcriptome data, were assessed to determine stable reference genes for qRT-PCR analysis of litchi pericarps from different varieties, with differing postharvest storage, and under pathogenic inoculation. Ct values, Genorm, Normfind, and Reffinder algorithms, were used to identify the most stable genes. The results showed that GAGA-25 was the most stable gene for comparing different varieties of fresh pericarp, HDAC9 was the most stable gene for postharvest pericarp, STAM was the most stable for inoculated pericarp. Among the candidate reference genes, GAGA-25 was the most stable reference gene across the complete sample set.Conclusion: This study evaluated reference gene stability for qRT-PCR with litchi pericarp. This work supplies a foundation for qPCR use in future gene function and molecular mechanism studies of litchi pericarp browning.

scholarly journals Comparison of Reliable Reference Genes Following Different Hormone Treatments by Various Algorithms for qRT-PCR Analysis of Metasequoia

2018 ◽  
Vol 20 (1) ◽  
pp. 34 ◽  
Author(s):  
Jing-Jing Wang ◽  
Shuo Han ◽  
Weilun Yin ◽  
Xinli Xia ◽  
Chao Liu
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Elongation Factor ◽  
Pcr Analysis ◽  
Qrt Pcr ◽  
Gene Normalization ◽  
Accurate Normalization ◽  
Suitable Reference ◽  
Different Tissues ◽  
Gene Expression Levels

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is the most sensitive technique for evaluating gene expression levels. Choosing appropriate reference genes for normalizing target gene expression is important for verifying expression changes. Metasequoia is a high-quality and economically important wood species. However, few systematic studies have examined reference genes in Metasequoia. Here, the expression stability of 14 candidate reference genes in different tissues and following different hormone treatments were analyzed using six algorithms. Candidate reference genes were used to normalize the expression pattern of FLOWERING LOCUS T and pyrabactin resistance-like 8. Analysis using the GrayNorm algorithm showed that ACT2 (Actin 2), HIS (histone superfamily protein H3) and TATA (TATA binding protein) were stably expressed in different tissues. ACT2, EF1α (elongation factor-1 alpha) and HIS were optimal for leaves treated with the flowering induction hormone solution, while Cpn60β (60-kDa chaperonin β-subunit), GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and HIS were the best reference genes for treated buds. EF1α, HIS and TATA were useful reference genes for accurate normalization in abscisic acid-response signaling. Our results emphasize the importance of validating reference genes for qRT-PCR analysis in Metasequoia. To avoid errors, suitable reference genes should be used for different tissues and hormone treatments to increase normalization accuracy. Our study provides a foundation for reference gene normalization when analyzing gene expression in Metasequoia.

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