Identification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca’s response to salinity

Abstract Quantitative real-time polymerase chain reaction (qPCR) using a stable reference gene is widely used for gene expression research. Suaeda glauca L. is a succulent halophyte and medicinal plant that is extensively used for phytoremediation and extraction of medicinal compounds. It thrives un...

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Autores principales:	Meng Wang, Tingting Ren, Prince Marowa, Haina Du, Zongchang Xu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/387bfe9a8f0e4c0a938b91e2c0abf062
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spelling	oai:doaj.org-article:387bfe9a8f0e4c0a938b91e2c0abf0622021-12-02T18:27:49ZIdentification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca’s response to salinity10.1038/s41598-021-88151-52045-2322https://doaj.org/article/387bfe9a8f0e4c0a938b91e2c0abf0622021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88151-5https://doaj.org/toc/2045-2322Abstract Quantitative real-time polymerase chain reaction (qPCR) using a stable reference gene is widely used for gene expression research. Suaeda glauca L. is a succulent halophyte and medicinal plant that is extensively used for phytoremediation and extraction of medicinal compounds. It thrives under high-salt conditions, which promote the accumulation of high-value secondary metabolites. However, a suitable reference gene has not been identified for gene expression standardization in S. glauca under saline conditions. Here, 10 candidate reference genes, ACT7, ACT11, CCD1, TUA5, UPL1, PP2A, DREB1D, V-H + -ATPase, MPK6, and PHT4;5, were selected from S. glauca transcriptome data. Five statistical algorithms (ΔCq, geNorm, NormFinder, BestKeeper, and RefFinder) were applied to determine the expression stabilities of these genes in 72 samples at different salt concentrations in different tissues. PP2A and TUA5 were the most stable reference genes in different tissues and salt treatments, whereas DREB1D was the least stable. The two reference genes were sufficient to normalize gene expression across all sample sets. The suitability of identified reference genes was validated with MYB and AP2 in germinating seeds of S. glauca exposed to different NaCl concentrations. Our study provides a foundational framework for standardizing qPCR analyses, enabling accurate gene expression profiling in S. glauca.Meng WangTingting RenPrince MarowaHaina DuZongchang XuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Meng Wang Tingting Ren Prince Marowa Haina Du Zongchang Xu Identification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca’s response to salinity
description	Abstract Quantitative real-time polymerase chain reaction (qPCR) using a stable reference gene is widely used for gene expression research. Suaeda glauca L. is a succulent halophyte and medicinal plant that is extensively used for phytoremediation and extraction of medicinal compounds. It thrives under high-salt conditions, which promote the accumulation of high-value secondary metabolites. However, a suitable reference gene has not been identified for gene expression standardization in S. glauca under saline conditions. Here, 10 candidate reference genes, ACT7, ACT11, CCD1, TUA5, UPL1, PP2A, DREB1D, V-H + -ATPase, MPK6, and PHT4;5, were selected from S. glauca transcriptome data. Five statistical algorithms (ΔCq, geNorm, NormFinder, BestKeeper, and RefFinder) were applied to determine the expression stabilities of these genes in 72 samples at different salt concentrations in different tissues. PP2A and TUA5 were the most stable reference genes in different tissues and salt treatments, whereas DREB1D was the least stable. The two reference genes were sufficient to normalize gene expression across all sample sets. The suitability of identified reference genes was validated with MYB and AP2 in germinating seeds of S. glauca exposed to different NaCl concentrations. Our study provides a foundational framework for standardizing qPCR analyses, enabling accurate gene expression profiling in S. glauca.
format	article
author	Meng Wang Tingting Ren Prince Marowa Haina Du Zongchang Xu
author_facet	Meng Wang Tingting Ren Prince Marowa Haina Du Zongchang Xu
author_sort	Meng Wang
title	Identification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca’s response to salinity
title_short	Identification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca’s response to salinity
title_full	Identification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca’s response to salinity
title_fullStr	Identification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca’s response to salinity
title_full_unstemmed	Identification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca’s response to salinity
title_sort	identification and selection of reference genes for gene expression analysis by quantitative real-time pcr in suaeda glauca’s response to salinity
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/387bfe9a8f0e4c0a938b91e2c0abf062
work_keys_str_mv	AT mengwang identificationandselectionofreferencegenesforgeneexpressionanalysisbyquantitativerealtimepcrinsuaedaglaucasresponsetosalinity AT tingtingren identificationandselectionofreferencegenesforgeneexpressionanalysisbyquantitativerealtimepcrinsuaedaglaucasresponsetosalinity AT princemarowa identificationandselectionofreferencegenesforgeneexpressionanalysisbyquantitativerealtimepcrinsuaedaglaucasresponsetosalinity AT hainadu identificationandselectionofreferencegenesforgeneexpressionanalysisbyquantitativerealtimepcrinsuaedaglaucasresponsetosalinity AT zongchangxu identificationandselectionofreferencegenesforgeneexpressionanalysisbyquantitativerealtimepcrinsuaedaglaucasresponsetosalinity
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Identification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca’s response to salinity

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