Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling

Abstract Chinese chive (Allium tuberosum) is widely cultivated around the world for its unique flavor, nutrient, and medicinal values, yet its molecular mechanism on flavor formation and other metabolic pathways remains intangible. The elucidation of these complex processes begins with investigating...

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Autores principales:	Jing Tong, Manman Hu, Beibei Han, Yanhai Ji, Baoju Wang, Hao Liang, Mingchi Liu, Zhanhui Wu, Ning Liu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/770580f5fbbe4ef99f4928480c441e91
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spelling	oai:doaj.org-article:770580f5fbbe4ef99f4928480c441e912021-12-02T18:51:52ZDetermination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling10.1038/s41598-021-95849-z2045-2322https://doaj.org/article/770580f5fbbe4ef99f4928480c441e912021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-95849-zhttps://doaj.org/toc/2045-2322Abstract Chinese chive (Allium tuberosum) is widely cultivated around the world for its unique flavor, nutrient, and medicinal values, yet its molecular mechanism on flavor formation and other metabolic pathways remains intangible. The elucidation of these complex processes begins with investigating the expression of the genes of interest, however the appropriate reference genes (RGs) for normalizing the gene expression are still unavailable in A. tuberosum. To fill this lacuna, transcriptome-wide screening was undertaken to identify the most stable genes according to the analysis of their FPKM values. The expression stability of the RGs was further evaluated using geNorm, NormFinder, BestKeeper, and RefFinder algorithms. The comprehensive analysis showed that GLY1 and SKP1, instead of two traditionally used RGs (eIF1α and ACT2), were the most stable genes across diverse A. tuberosum tissues, indicating the necessity to carefully validate the stability of RGs prior to their use for normalizations. As indicated by geNorm, the normalizations with at least two RGs could give more accurate results. qRT-PCR experiments were conducted with randomly selected genes, demonstrating that normalization with a combination of GLY1 and SKP1 resulted in reliable normalization results. Our finding represents the first attempt toward establishing a standardized qRT-PCR analysis in this economically important vegetable.Jing TongManman HuBeibei HanYanhai JiBaoju WangHao LiangMingchi LiuZhanhui WuNing LiuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jing Tong Manman Hu Beibei Han Yanhai Ji Baoju Wang Hao Liang Mingchi Liu Zhanhui Wu Ning Liu Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling
description	Abstract Chinese chive (Allium tuberosum) is widely cultivated around the world for its unique flavor, nutrient, and medicinal values, yet its molecular mechanism on flavor formation and other metabolic pathways remains intangible. The elucidation of these complex processes begins with investigating the expression of the genes of interest, however the appropriate reference genes (RGs) for normalizing the gene expression are still unavailable in A. tuberosum. To fill this lacuna, transcriptome-wide screening was undertaken to identify the most stable genes according to the analysis of their FPKM values. The expression stability of the RGs was further evaluated using geNorm, NormFinder, BestKeeper, and RefFinder algorithms. The comprehensive analysis showed that GLY1 and SKP1, instead of two traditionally used RGs (eIF1α and ACT2), were the most stable genes across diverse A. tuberosum tissues, indicating the necessity to carefully validate the stability of RGs prior to their use for normalizations. As indicated by geNorm, the normalizations with at least two RGs could give more accurate results. qRT-PCR experiments were conducted with randomly selected genes, demonstrating that normalization with a combination of GLY1 and SKP1 resulted in reliable normalization results. Our finding represents the first attempt toward establishing a standardized qRT-PCR analysis in this economically important vegetable.
format	article
author	Jing Tong Manman Hu Beibei Han Yanhai Ji Baoju Wang Hao Liang Mingchi Liu Zhanhui Wu Ning Liu
author_facet	Jing Tong Manman Hu Beibei Han Yanhai Ji Baoju Wang Hao Liang Mingchi Liu Zhanhui Wu Ning Liu
author_sort	Jing Tong
title	Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling
title_short	Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling
title_full	Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling
title_fullStr	Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling
title_full_unstemmed	Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling
title_sort	determination of reliable reference genes for gene expression studies in chinese chive (allium tuberosum) based on the transcriptome profiling
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/770580f5fbbe4ef99f4928480c441e91
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Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling

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