Selection of candidate reference genes and validation for real-time PCR studies in rice plants exposed to low temperatures

Auler, Priscila Ariane; Benitez, Letícia Carvalho; Amaral, Marcelo Nogueira do; Vighi, Isabel Lopes; Rodrigues, Grazieli; Maia, Luciano Carlos da; Braga, Eugênia Jacira Bolacel

doi:10.4238/gmr16029695

Cited by 8 publications

(4 citation statements)

References 47 publications

(50 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The UBQ gene belongs to the ubiquitin gene family, which affects many important biological processes, including cell cycle regulation, growth and apoptosis, signal transduction, and immune responses. Because of its high sequence homology and the fact it is highly conserved, UBQ has been used as a reference gene for rice 36 , black fungus 37 , and cucumber 32 . Our data also indicated that TUB was the most stably expressed reference gene for the H 2 O 2 and drought treatments.…”

Section: Discussionmentioning

confidence: 99%

Reference gene selection for qRT-PCR analyses of luffa (Luffa cylindrica) plants under abiotic stress conditions

Chen

Wang

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Selecting suitable internal reference genes is an important prerequisite for the application of quantitative real-time PCR (qRT-PCR). However, no systematic studies have been conducted on reference genes in luffa. In this study, seven reference genes were selected, and their expression levels in luffa plants exposed to various simulated abiotic stresses [i.e., cold, drought, heat, salt, H2O2, and abscisic acid (ABA) treatments] were analyzed by qRT-PCR. The stability of the reference gene expression levels was validated using the geNorm, NormFinder, BestKeeper, and RefFinder algorithms. The results indicated that EF-1α was the most stably expressed and suitable reference gene overall and for the heat, cold, and ABA treatments. Additionally, UBQ expression was stable following the salt treatment, whereas TUB was identified as a suitable reference gene for H2O2 and drought treatments. The reliability of the selected reference genes was verified by analyzing the expression of copper/zinc superoxide dismutase (Cu/Zn-SOD) gene in luffa. When the most unstable reference genes were used for data normalizations, the resulting expression patterns had obvious biases when compared with the expression patterns for the most ideal reference genes used alone or combined. These results will be conducive to more accurate quantification of gene expression levels in luffa.

show abstract

Section: Discussionmentioning

confidence: 99%

Reference gene selection for qRT-PCR analyses of luffa (Luffa cylindrica) plants under abiotic stress conditions

Chen

Wang

et al. 2021

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The UBQ gene belongs to the ubiquitin gene family, which affects many important biological processes, including cell cycle regulation, growth and apoptosis, signal transduction, and immune responses. Because of its high sequence homology and the fact it is highly conserved, UBQ has been used as a reference gene for rice [36], tomato [37], and cucumber [38]. Our data also indicated that TUB was the most stably expressed reference gene for the H2O2 and drought treatments.…”

Section: Discussionmentioning

confidence: 55%

Reference Gene Selection for qRT-PCR Analyses of Luffa (Luffa cylindrica) Plants Under Abiotic Stress Conditions

chen

Wang

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Quantitative real-time PCR (qRT-PCR) is one of the preferred methods for analyzing gene expression, and selecting suitable internal reference genes is an important prerequisite for the application of this technology. However, no systematic studies have been conducted on reference genes in luffa, resulting in limited investigations of luffa gene expression. Results: In this study, seven reference genes ( ACT , TUA , TUB , EF-1α , GAPDH , UBQ , and 18S ) were selected, and their expression levels in luffa plants exposed to various simulated abiotic stresses [i.e., cold, drought, heat, salt, H 2 O 2 , and abscisic acid (ABA) treatments] were analyzed by qRT-PCR. The stability of the reference gene expression levels was validated using the geNorm, NormFinder, BestKeeper, and RefFinder algorithms. The results indicated that EF-1α was the most stably expressed and suitable reference gene overall and for the heat, cold, and ABA treatments. Additionally, UBQ expression was stable following the salt treatment, whereas TUB was identified as a suitable reference gene for H 2 O 2 and drought treatments. In contrast, GAPDH was revealed as an unsuitable reference gene overall and for the heat, salt, H 2 O 2 , ABA, and drought treatments. Regarding the cold treatment, TUA was identified as an unsuitable reference gene. The reliability of the selected reference genes was verified by analyzing the expression of copper/zinc superoxide dismutase ( Cu/Zn-SOD ) gene in luffa. When the most unstable reference genes were used for data normalizations, the resulting expression patterns had obvious biases when compared with the expression patterns for the most ideal reference genes used alone or combined. Conclusions: The study data were used to compile a list of suitable reference genes for qRT-PCR analyses of the gene expression in luffa plants exposed to abiotic stresses. This work may provide the basis for future qRT-PCR-based investigations of the transcription of important functional genes in luffa.

show abstract

“…There is, however, no universal reference gene suitable for all species or experimental conditions [34]. Although many studies have assessed reference genes in different tissues and development stages of rice plants, and after subjecting plants to different kinds of stress [28,[35][36][37][38][39][40][41], to the best of our knowledge, no one has attempted to identify stable reference genes in the leaves of SRBSDVinfected rice plants.…”

Section: Discussionmentioning

confidence: 99%

“…We also found UBQ10 and EF1α to be reliable reference genes in the leaves of SRBSDV-infected rice plants. EF1α has been identified as a stable reference gene in rice subject to low temperatures [36], and UBQ10 has been recommended as a reliable reference gene in rice plant leaves subject to salt stress [28]. GAPDH is commonly regarded as the "classical" reference gene [45], and has been suggested as a reliable reference gene in rice seedlings suffering from iron toxicity [35].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of reference genes and expression of key genes involved in the isoprenoid metabolic pathway of rice leaves after infection by the Southern rice black-streaked dwarf virus

Qiu

Ding

et al. 2019

Mol Biol Rep

View full text Add to dashboard Cite

The Southern rice black-streaked dwarf virus (SRBSDV), a novel Fijivirus, poses a major threat to rice production in East Asia. Analysis of the gene expression of SRBSDV-infected rice plants may reveal the molecular basis of interactions between the virus, its vector and rice plants. Reliable reference genes are required for accurate qRT-PCR analysis. However, no reliable, valid reference genes for examining gene expression in SRBSDV-infected rice plants have so far been identified. We examined the expression of eight candidate reference genes in the leaves of SRBSDV-infected, and healthy, rice plants at different points in time after virus inoculation. We used four dedicated algorithms, geNorm, BestKeeper, NormFinder and RefFinder, to evaluate the performance of these candidate genes. The RefFinder results indicate that 18S, EF1α and UBQ10 are suitable reference genes. In addition, we used these three reference genes to analyze the expression of key genes involved in the isoprenoid metabolic pathway in rice leaves after infection by SRBSDV. The results of this analysis reveal that SRB-SDV may suppress the production of the rice plant volatiles that attract natural enemies of its vector Sogatella furcifera, thereby increasing the likelihood of pathogen transmission.

show abstract

Selection of candidate reference genes and validation for real-time PCR studies in rice plants exposed to low temperatures

Cited by 8 publications

References 47 publications

Reference gene selection for qRT-PCR analyses of luffa (Luffa cylindrica) plants under abiotic stress conditions

Reference gene selection for qRT-PCR analyses of luffa (Luffa cylindrica) plants under abiotic stress conditions

Reference Gene Selection for qRT-PCR Analyses of Luffa (Luffa cylindrica) Plants Under Abiotic Stress Conditions

Evaluation of reference genes and expression of key genes involved in the isoprenoid metabolic pathway of rice leaves after infection by the Southern rice black-streaked dwarf virus

Contact Info

Product

Resources

About